How to check cDNA mouse embryonic fibroblast gene expression ?

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Donncha Dunican Popular answer

Hi,

The columns called "Exp_....." are the expression data from cDNA microarrays. Arbitrary hybridisation values in this column. Look at column3 to search for your gene. ActB is a very highly expressed gene in MEF. NeuroD1 is low in MEF.

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Donncha Dunican

There is probably something software-wise out there. But the easiest way to do this (if I understand correctly) is to look at published data. There is some old (but perfectly usable) MEF gene expression data in this table here from a paper by Alexander Meissner and colleagues [http://www.nature.com/nature/journal/v454/n7205/extref/nature07107-s2.xls]. Plus, you get expression in NPC, ESC and many other cell types. Note, not all genes are included here as they were looking at expression of genes linked to high density CpG islands - but it is a good start for you. Hope this helps, Good luck, Donncha.

Dewi Yuliana

Thanks very much, I want to find my gene in cDNA mouse embryonic fibroblast before I do amplification. What the meaning concentration in that table especially mouse embryonic fibroblast (MEF) ?

Thanks very much, but when I checked, why I did not find ActB in the table? I just found NeuroD1. But there are two kind. Cerk1 (Neurogenic differentiation 1/Neurod1) = 0,0353, and Neurod1 (Sperm specific antigen 2/Ssfa2) = 0,0306.

Try this excel spreadsheet.

http://www.nature.com/nature/journal/v448/n7153/extref/nature06008-s5.xls

Compare "ESC expression" vs. "MEF expression".

Centa2 and smap1 are there. There is no data for adap2.

Good luck,

It is the same journal with Supplementary Data for Meissner et al. "Genome-scale DNA methylation maps of pluripotent and differentiated cells" ..? thanks

Hi, yes it is expression microarray data from the same paper by Mikkelsen. I gave you the wrong Excel the first time.

Thanks very much, Now I understood way I failed amplify centa2 because it expression was low in microarray in MEF. compare with smap1. I will try smap1 gene. Your information help me so much in my research..